This is intended as a minimal viable product, to pre-run and troubleshoot with a smaller data set. Data size: 489 rodent species out of 2200 species. (Final version will probably have 900 - 1100 data points, 50% of all Rodentia species) Goals: 1.Find the consensus Rodentia tree 2.Do ancestral state reconstruction and plot. 3.Find out other tests of interest to run.
I realize that 1000 trees are not sufficient to resolve the phylogeny, as shown below. Therefore I did ancestral state reconstruction on a randomly chosen tree. For the final version, I plan to run on 10,000 trees. I will settle with a random tree for now because 10,000 trees takes significantly longer time to process.
I will also look into recent rodent literature to see if others have resolved a better tree and if there is anything that I can learn from.
tree_readin = read.nexus('1028_output.nex')
tree2 = random.tree<-sample(tree_readin,size=1)[[1]]
print(tree2)
##
## Phylogenetic tree with 468 tips and 467 internal nodes.
##
## Tip labels:
## Glirulus_japonicus, Chaetocauda_sichuanensis, Selevinia_betpakdalaensis, Glis_glis, Graphiurus_lorraineus, Graphiurus_surdus, ...
##
## Rooted; includes branch lengths.
plot(tree2)
consensusTree = consensus(tree_readin, p = 0.5, check.labels = FALSE)
plot(consensusTree)